HIPS 2022 README
Jensina Davis
2023-09-07
This is the documentation for the HIPS 2022 Dataset.
Variable Definitions And Notes
Each of the following variables includes notes on how the trait was collected and the original data file the data was taken from and any specific notes regarding errors or data cleaning done. Variables are listed by the name used in the final version of the data set. For all quantitative variables, observations an order of magnitude larger than other observations, those appearing as extreme outliers in histograms, and those appearing outside the primary bounds of the distribution for the location were dropped from the data set.
qrCode
This is the QR code assigned to the plot. This information for the Lincoln location hybrids was taken from the sheet ‘Combined Dataset’ in the file ‘Summary of Lincoln Hybrid HIPS 2022 Data.xlsx’. This information for hybrids in the Scottsbluff, Missouri Valley, and North Platte locations was taken from the file ‘HybridHIPS_plotlevelNIR$_v2.6.csv’. This information for the Ames and Crawfordsville locations was taken from the unique id field in the sheets ‘RawData (4-Row)’ and ‘RawData (2-Row)’ in the file ‘YTMC_Lisa_Plot_Coordinates_v4.xlsx’.
location
This is the location the plot was grown in. In the case of North Platte is treated as 3 separate locations to account for the duplication of range and row numbers across the different irrigation levels, and so that irrigation was not nested within this location, similar to the other locations. This information for the Lincoln location hybrids was taken from the sheet ‘Combined Dataset’ in the file ‘Summary of Lincoln Hybrid HIPS 2022 Data.xlsx’. This information for the hybrids in the Scottsbluff, Missouri Valley, and North Platte locations was taken from the file ‘HybridHIPS_plotlevelNIR$_v2.6.csv’. This information for the Ames and Crawfordsville locations was taken from the unique id field in the sheets ‘RawData (4-Row)’ and ‘RawData (2-Row)’ in the file ‘YTMC_Lisa_Plot_Coordinates_v4.xlsx’ and uses the letter contained in the QR.
sublocation
This is the field within the location the plot was grown in. This information for the Lincoln location hybrids was taken from the sheet ‘Combined Dataset’ in the file ‘Summary of Lincoln Hybrid HIPS 2022 Data.xlsx’. This information for the hybrids in the Scottsbluff, Missouri Valley, and North Platte locations was taken from the file ‘HybridHIPS_plotlevelNIR$_v2.6.csv’. This is information for the Ames and Crawfordsville locations was determined based on experiment code, which was dependent on the nitrogen level and the field maps.
irrigationProvided
This is the total amount of water in inches provided to the plot via irrigation over the course of the growing season. This information for the Lincoln location hybrids was taken from the sheet ‘Combined Dataset’ in the file ‘Summary of Lincoln Hybrid HIPS 2022 Data.xlsx’. This information for the North Platte location was taken from the files ‘HybridHIPS_plotlevelNIR$_v2.6.csv’ and ‘weather/2022_HIPS_Irrigation_North_Platte.xlsx’ and from personal communications for Missouri Valley and Scottsbluff locations.
nitrogenTreatment
This is the categorical level of nitrogen fertilizer the plot was supplied with. Plots denoted as ‘Low’ received a rate of 75 lbs/acre. Plots denoted as ‘Medium’ received a rate of 150 lbs/acre, except at Missouri Valley, where the ‘Medium’ nitrogen treatment received a rate of 175 lbs/acre. Plots denoted as ‘High’ received a rate of 225 lbs/acre, except in Ames, where plots in the ‘High’ treatment received 250 lbs/acre. In Scottsbluff, based on the yield and grain protein content data, the labels in the plot maps and the QR codes for high and low nitrogen treatments were flipped. The QR codes are as originally scanned, and this field reflects the correction of this error. This information for the Lincoln location hybrids was taken from the sheet ‘Combined Dataset’ in the file ‘Summary of Lincoln Hybrid HIPS 2022 Data.xlsx’. This information for the hybrids in the Scottsbluff, Missouri Valley, and North Platte locations was taken from the file ‘HybridHIPS_plotlevelNIR$_v2.6.csv’. This is information for the Ames and Crawfordsville locations was determined based on experiment code, which was dependent on the nitrogen level.
poundsOfNitrogenPerAcre
This is the rate of nitrogen fertilization the plot received, in
pounds per acre. This information for each plot was based on the data
documentation for each field and the nitrogenTreatment and
location the plot belongs to.
experiment
This is the experiment code the plot belonged to, corresponding to nitrogen levels within a population (i.e. hybrid or inbred) within a location for the Missouri Valley, Ames, and Crawfordsville locations. This information was taken from the ‘Basic info’ sheet in the file ‘YTMC_Lisa_Plot_Coordinates_v4.xlsx’. Experiment codes were not assigned to Lincoln, North Platte, and Scottsbluff locations.
plotLength
This is the planted length of the plot in feet. This information for North Platte was taken from the sheets ‘No Irr Data’, ‘Reduced Irr Data’, and ‘Full Data’ in the file ‘2022_Schnable_HIPS_data_v4.xlsx’. This information for the Lincoln location was taken from personal communications with Jon Turkus. This information for Missouri Vallley, Scottsbluff, Ames, and Crawfordsville was taken from personal communications with Lisa Coffey.
totalStandCount
This is the number of standing plants in two rows. In the case of hybrids, this is the middle two rows of the four-row plot, and in the case of inbreds, both rows of the two-row plot. This information (‘Stand’) for Missouri Valley, Crawfordsville, and Ames was taken from the sheets ‘RawData (4-Row)’ and ‘RawData (2-Row)’ for hybrids and inbreds, respectively, in the file ‘YTMC_Lisa_Plot_Coordinates_v4.xlsx’. This information for North Platte was taken from the sheets ‘No Irr Data’, ‘Reduced Irr Data’, and ‘Full Data’ in the file ‘2022_Schnable_HIPS_data_v4.xlsx’ as the sum of the columns ‘R1 Stand’ and ‘R2 Stand’. This data was not collected for the hybrid field at Lincoln.
block
This is the block number of the plot within a sublocation. These values were assigned based on the location, sublocation, and rep number [not included] associated with a plot. This information for the Lincoln location hybrids was taken from the sheet ‘Combined Dataset’ in the file ‘Summary of Lincoln Hybrid HIPS 2022 Data.xlsx’. This information for the hybrids in the Scottsbluff, Missouri Valley, and North Platte locations was taken from the file ‘HybridHIPS_plotlevelNIR$_v2.6.csv’. This information for the Missouri Valley, Ames, and Crawfordsville locations was taken from the sheets ‘RawData (4-Row)’ and ‘RawData (2-Row)’ in the file ‘YTMC_Lisa_Plot_Coordinates_v4.xlsx’. The rep numbers were misassigned in the QR codes used for ear phenotypes and NIR measurements for the Missouri Valley hybrids, and have been corrected in the block column in the dataset.
row
This is the row number within a sublocation the plot was
located in. This information for the Lincoln location hybrids was taken
from the sheet ‘Combined Dataset’ in the file ‘Summary of Lincoln Hybrid
HIPS 2022 Data.xlsx’. This information for hybrids in the Scottsbluff,
Missouri Valley, and North Platte locations was taken from the file
‘HybridHIPS_plotlevelNIR$_v2.6.csv’. This information for the Ames and
Crawfordsville locations was taken from the sheets ‘RawData (4-Row)’ and
‘RawData (2-Row)’ in the file ‘YTMC_Lisa_Plot_Coordinates_v4.xlsx’. In
some files, this is denoted as ‘Pass’.
range
This is the range number within a sublocation the plot
was located in. This information for the Lincoln location hybrids was
taken from the sheet ‘Combined Dataset’ in the file ‘Summary of Lincoln
Hybrid HIPS 2022 Data.xlsx’. This information for the hybrids in the
Scottsbluff, Missouri Valley, and North Platte locations was taken from
the file ‘HybridHIPS_plotlevelNIR$_v2.6.csv’. This information for the
Ames and Crawfordsville locations was taken from the sheets ‘RawData
(4-Row)’ and ‘RawData (2-Row)’ in the file
‘YTMC_Lisa_Plot_Coordinates_v4.xlsx’.
plotNumber
This is the number assigned to the plot. This information for the Lincoln location hybrids was taken from the sheet ‘Combined Dataset’ in the file ‘Summary of Lincoln Hybrid HIPS 2022 Data.xlsx’.This information for hybrids in the Scottsbluff, Missouri Valley, and North Platte locations was taken from the file ‘HybridHIPS_plotlevelNIR$_v2.6.csv’. This information for the Ames and Crawfordsville locations was taken from the unique id field in the sheets ‘RawData (4-Row)’ and ‘RawData (2-Row)’ in the file ‘YTMC_Lisa_Plot_Coordinates_v4.xlsx’ and uses the number sequence at the end of the QR.
latituded
This is the latitude of the plot. This information for Missouri Valley, Crawfordsville, and Ames was taken from the sheets ‘RawData (4-Row)’ and ‘RawData (2-Row)’ for hybrids and inbreds, respectively, in the file ‘YTMC_Lisa_Plot_Coordinates_v4.xlsx’.
longitude
This is the longitude of the plot. This information for Missouri Valley, Crawfordsville, and Ames was taken from the sheets ‘RawData (4-Row)’ and ‘RawData (2-Row)’ for hybrids and inbreds, respectively, in the file ‘YTMC_Lisa_Plot_Coordinates_v4.xlsx’.
genotype
This is the genotype grown in the plot.This information for the Lincoln location hybrids was taken from the sheet ‘Combined Dataset’ in the file ‘Summary of Lincoln Hybrid HIPS 2022 Data.xlsx’.This information for hybrids in the Scottsbluff, Missouri Valley, and North Platte locations was taken from the file ‘HybridHIPS_plotlevelNIR$_v2.6.csv’. This information for the Ames and Crawfordsville locations was taken from the sheets ‘RawData (4-Row)’ and ‘RawData (2-Row)’ in the file ‘YTMC_Lisa_Plot_Coordinates_v4.xlsx’. In Missouri Valley, Ames, and Crawfordsville, some plots’ genotypes were listed as ‘SOLAR’ 1-4, with no note on the hybrid grown in the plot. These plots’ genotypes were transformed to NA, with a note on the solar panel in the notes field.
plantingDate
This is the date the plot was planted.
anthesisDate
This is the date when 50% of plants in the plot reached anthesis (tasseling). This information for the Lincoln location hybrids was taken from the sheet ‘Combined Dataset’ in the file ‘Summary of Lincoln Hybrid HIPS 2022 Data.xlsx’. This information for the Scottsbluff location hybrids was taken from the sheet ‘Hybrid_flowering data’ in the file ‘Corn_data_Scottsbluff-2022_rk_11.11.2022’. This information for the North Platte location was taken from the sheets ‘Full Data’, ‘Reduced Irr Data’, and ‘No Irr Data’ in the file ‘2022_Schnable_HIPS_data_v4.xlsx’. This data was not collected at the Missouri Valley, Crawfordsville, and Ames locations.
silkDate
This is the date when 50% of plants in the plot reached silking. This information for the Lincoln location hybrids was taken from the sheet ‘Combined Dataset’ in the file ‘Summary of Lincoln Hybrid HIPS 2022 Data.xlsx’. This information for the Scottsbluff hybrids location was taken from the sheet ‘Hybrid_flowering data’ in the file ‘Corn_data_Scottsbluff-2022_rk_11.11.2022’. This information for the North Platte location was taken from the sheets ‘Full Data’, ‘Reduced Irr Data’, and ‘No Irr Data’ in the file ‘2022_Schnable_HIPS_data_v4.xlsx’. This data was not collected at the Missouri Valley, Crawfordsville, and Ames locations.
daysToAnthesis
This is the number of days between the plantingDate and
anthesisDate.
daysToSilk
This is the number of days between the plantingDate and
silkDate. Plots 1397 at North Platte and 1156 at
Scottsbluff were visual outliers in scatterplots and were dropped.
anthesisSilkingInterval
This is the anthesis-silking interval in days, and is calculated as
the difference between the silkDate and
anthesisDate for a plot. Negative values indicate that
silking occurred prior to anthesis. Values greater than 20 days were
visual outliers in the histogram and were dropped.
GDDToAnthesis
This is the cumulative number of GDDs for the location on between
plantingDate and anthesisDate for the plot.
GDDs were calculated using temperatures in Fahrenheit with a crop base
temperature of 50 degrees and a crop maximum temperature of 86 degrees.
Where there was a weather station data for the field, the temperatures
recorded therein were used to calculate the daily minimum and maximum
temperatures and converted from Celsius if needed. In cases where there
was missing data or the maximum temperature was above the maximum
observed temperature for the nearest town, data was imputed from DAYMET
using the latitude and longitude of the center of the plot. In
Crawfordsville, there was no weather station but a G2F field was located
nearby. The weather data for Crawfordsville was accessed from doi:10.25739/3d3g-pe51 for
the site IAH1. This data was previously cleaned and imputed using data
from NASA. Values less than 900 GDD were visual outliers in the
histogram and were dropped.
GDDToSilk
This is the cumulative number of GDDs for the location on between
plantingDate and silkDate for the plot. GDDs
were calculated using temperatures in Fahrenheit with a crop base
temperature of 50 degrees and a crop maximum temperature of 86 degrees.
Where there was a weather station data for the field, the temperatures
recorded therein were used to calculate the daily minimum and maximum
temperatures and converted from Celsius if needed. In cases where there
was missing data or the maximum temperature was above the maximum
observed temperature for the nearest town, data was imputed from DAYMET.
In Crawfordsville, there was no weather station but a G2F field was
located nearby. The weather data for Crawfordsville was accessed from doi:10.25739/3d3g-pe51 for
the site IAH1. This data was previously cleaned and imputed using data
from NASA. Values greater than 1900 GDDs were visual outliers in the
histogram and were dropped.
anthesisSilkingIntervalGDD
This is the cumulative number of GDDs for the location on between
anthesisDate and silkDate for the plot.
Negative values indicate silking occurred prior to anthesis. GDDs were
calculated using temperatures in Fahrenheit with a crop base temperature
of 50 degrees and a crop maximum temperature of 86 degrees. Where there
was a weather station data for the field, the temperatures recorded
therein were used to calculate the daily minimum and maximum
temperatures and converted from Celsius if needed. In cases where there
was missing data or the maximum temperature was above the maximum
observed temperature for the nearest town, data was imputed from DAYMET.
In Crawfordsville, there was no weather station but a G2F field was
located nearby. The weather data for Crawfordsville was accessed from doi:10.25739/3d3g-pe51 for
the site IAH1. This data was previously cleaned and imputed using data
from NASA. Weather station data can be accessed in the folder
data/weather. Values greater than 450 were visual outliers in the
histogram and were dropped.
earHeight
This is the height in centimeters of the point of attachment to the stalk of the top ear of one plant from the plot (in the case of Scottsbluff) or the average of this measurement for two plants from the plot in Lincoln. All measurements from plants noted as stunted or without a silk were marked as missing data prior to calculation. This information for the Lincoln location hybrids was taken from the sheet ‘Combined Dataset’ in the file ‘Summary of Lincoln Hybrid HIPS 2022 Data.xlsx’. For Scottsbluff hybrids, this data was taken from the sheet ‘Hybrid_height data’ from the file ‘Corn_data_Scottsbluff-2022_rk_11.11.2022’ and converted from inches. This information for the North Platte location was taken from the sheets ‘Full Data’, ‘Reduced Irr Data’, and ‘No Irr Data’ in the file ‘2022_Schnable_HIPS_data_v4.xlsx’ and converted from meters. Plots 5244, 5283, 5141 in Lincoln were dropped as they appeared to be an order of magnitude too low. This information for Missouri Valley was taken from the file ‘Plant_data_MO_Valley_2022.xlsx’. The data was collected going through the field by range and row, so these are correct, but in this file the replicate numbers were inverted, so the replicate numbers and genotypes for a plot at a given range was taken from the yield data for Missouri Valley. This information for Ames was taken from the file ‘Plant_data_Ames_2022.xlsx.’ This information for Crawfodsville was taken from the file ‘Plant_data_Crawfordsville.xlsx’. Ear heights less than 35 cm were visual outliers in the histogram and were dropped.
flagLeafHeight
This is the height in centimeters of the point of attachment to the stalk of the flag leaf of one plant from the plot (in the case of Scottsbluff) or the average of this measurement for two plants from the plot in Lincoln. All measurements from plants noted as stunted or without a silk were marked as missing data prior to calculation. This information for the Lincoln location hybrids was taken from the sheet ‘Combined Dataset’ in the file ‘Summary of Lincoln Hybrid HIPS 2022 Data.xlsx’. For Scottsbluff hybrids , this data was taken from the sheet ‘Hybrid_height data’ from the file ‘Corn_data_Scottsbluff-2022_rk_11.11.2022’ and converted from inches. This information for the North Platte location was taken from the sheets ‘Full Data’, ‘Reduced Irr Data’, and ‘No Irr Data’ in the file ‘2022_Schnable_HIPS_data_v4.xlsx’ and converted from meters. This information for Missouri Valley was taken from the file ‘Plant_data_MO_Valley_2022.xlsx’. This information for Ames was taken from the file ‘Plant_data_Ames_2022.xlsx.’ This information for Crawfordsville was taken from the file ‘Plant_data_Crawfordsville.xlsx’. Plot 1322 at Scottsbluff was dropped due to having a value 60 cm (~1.9 feet) greater than all other observations. Flag leaf heights less than 50 cm were visual outliers in the histogram and were dropped.
plantDensity
This is density of the plants per acre in the plot. This is
calculated as the mean number of plants per row (i.e., one-half of
totalStandCount) scaled to be equivalent to 1/1000th of an
acre (a plot length of 17.5 feet with an assumed spacing of 30”) and
multiplied by 1000.
combineYield
This is the weight, in pounds, of the grain harvested from the inner two rows of the plot by the combine. Inbred plots were not harvested by the combine. This information for the Lincoln location was taken from the sheet ‘Combined Dataset’ in the file ‘Summary of Lincoln Hybrid HIPS 2022 Data.xlsx’. For the Scottsbluff location, this information was taken from the file ‘Dipak Corn22_HM.xlsx’. This information for the North Platte location was taken from the sheets ‘Full Data’, ‘Reduced Irr Data’, and ‘No Irr Data’ in the file ‘2022_Schnable_HIPS_data_v4.xlsx.’ This information for the Missouri Valley, Crawfordsville, and Ames locations was taken from the sheet ‘RawData (4-Row)’ in the file ‘YTMC_Lisa_Plot_Coordinates_v4.xlsx’. All observations with any of the following values in combineNotes were dropped: “Left row ran over”, “Right row gone”, “Run over”, “Clog”, “Animal damage”, “Animal damage, not enough grain for accurate moisture”, “One row”, “Same as last”, “11/9/2022, 11:45:04 AM, Tare Warning, Test Weight: 5.75”, “Plot lost to belt issue”. Plot 250 in North Platte1 was also dropped, as it had a weight approximately twice all other values and appeared that 4 rows, instead of two, were potentially harvested. For the Missouri Valley, Ames, and Crawfordsville locations, this data was taken from the file ‘YTMC_Lisa_Plot_Coordinates_v4.xlsx’.
yieldPerAcre
This is the yield, in 56-lb bushels of grain at 15.5% moisture per
acre. This value was calculated from the combineYield,
combineMoisture, and plotLen values for the
plot. This calculation assumes a 30” row spacing.
combineMoisture
This is the moisture content, in percent, on a wet (fresh-weight) basis, measured by the combine at the time of harvesting the plot. Inbred plots were not harvested by the combine. This information for the Lincoln location was taken from the sheet ‘Combined Dataset’ in the file ‘Summary of Lincoln Hybrid HIPS 2022 Data.xlsx’. For the Scottsbluff location, this information was taken from the file ‘Dipak Corn22_HM.xlsx’. This information for the North Platte location was taken from the sheets ‘Full Data’, ‘Reduced Irr Data’, and ‘No Irr Data’ in the file ‘2022_Schnable_HIPS_data_v4.xlsx.’ This information for the Missouri Valley, Crawfordsville, and Ames locations was taken from the sheet ‘RawData (4-Row)’ in the file ‘YTMC_Lisa_Plot_Coordinates_v4.xlsx’. All observations equal to zero or with any of the following values in combineNotes were dropped: “Left row ran over”, “Right row gone”, “Run over”, “Clog”, “Animal damage”, “Animal damage, not enough grain for accurate moisture”, “One row”, “Same as last”, “11/9/2022, 11:45:04 AM, Tare Warning, Test Weight: 5.75”, “Plot lost to belt issue”, “Water stress, not enough grain for accurate moisture”, “Not enough grain for accurate moisture”. Plot 250 in North Platte1 was also dropped, as it had a weight approximately twice all other values and appeared that 4 rows, instead of two, were potentially harvested. For the Missouri Valley, Ames, and Crawfordsville locations, this data was taken from the file ‘YTMC_Lisa_Plot_Coordinates_v4.xlsx’.
combineTestWeight
This is the test weight, e.g. the weight in pounds of a volumetric bushel (1.24 cubic feet), of the grain harvested from the plot by the combine. Inbred plots were not harvested by the combine. This information for the Lincoln location was taken from the sheet ‘Combined Dataset’ in the file ‘Summary of Lincoln Hybrid HIPS 2022 Data.xlsx’. For the Scottsbluff location, this information was taken from the file ‘Dipak Corn22_HM.xlsx’. This information for the North Platte location was taken from the sheets ‘Full Data’, ‘Reduced Irr Data’, and ‘No Irr Data’ in the file ‘2022_Schnable_HIPS_data_v4.xlsx.’ This information for the Missouri Valley, Crawfordsville, and Ames locations was taken from the sheet ‘RawData (4-Row)’ in the file ‘YTMC_Lisa_Plot_Coordinates_v4.xlsx’. All observations equal to zero or with any of the following values in combineNotes were dropped: “Left row ran over”, “Right row gone”, “Run over”, “Clog”, “Animal damage”, “Animal damage, not enough grain for accurate moisture”, “One row”, “Same as last”, “11/9/2022, 11:45:04 AM, Tare Warning, Test Weight: 5.75”, “Plot lost to belt issue”. Plot 250 in North Platte1 was also dropped, as it had a weight approximately twice all other values and appeared that 4 rows, instead of two, were potentially harvested. For the Missouri Valley, Ames, and Crawfordsville locations, this data was taken from the file ‘YTMC_Lisa_Plot_Coordinates_v4.xlsx’.
earLength
This is the mean length of the cob after shelling (i.e. with the kernels removed) of one ear from the plot. This information for hybrids and Missouri Valley inbreds was taken from the file ‘plotleveleardata_v2.csv’. Plot 426 in North Platte1 was dropped as all underlying observations were an order of magnitude larger than all other observations. This information for the Ames and Crawfordsville locations was taken from the files in the folder ‘5 Cob Traits Station’ and converted from millimeters to centimeters. For these two locations, when the ear had severe bending, a string was used to measure the length and this is denoted in the notes field.
earFillLength
This is the mean length filled with kernels on one ear from the plot in centimeters prior to shelling (i.e. with the kernels attached to the cob). This information for hybrids was taken from the file ‘plotleveleardata_v2.csv’. Plot 426 in North Platte1 was dropped as all underlying observations were an order of magnitude larger than all other observations, and the mean for plots 879 and 837 in North Platte2 was calculated from 3 (rather than 4) ears due to the observation for the fourth ear being an order of magnitude larger than all other observations. This data was not collected for the Ames and Crawfordsville locations. This data was initially not collected for ears phenotyped by the UNL team (North Platte, Scottsbluff, Lincoln, Missouri Valley), but began approximately one-third of the way through phenotyping the first location, Missouri Valley.
earWidth
This is the mean width of one ear from the plot in centimeters prior to shelling (i.e. with the kernels attached to the cob). This information for hybrids at the Scottsbluff, North Platte, Lincoln, and Missouri Valley was taken from the file ‘plotleveleardata_v2.csv’. Plot 426 in North Platte1 was dropped as all underlying observations were an order of magnitude larger than all other observations. Plot 6129 at Lincoln and plot 1585236 were calculated using 3 rather than 4 ears as the remaining observation was an order of magnitude larger than the other observations. This information for the Ames and Crawfordsville locations were taken from the files in the folder ‘3 Ear Traits Station’ and converted from millimeters to centimeters.
shelledCobWidth
This is the mean width of one cob from the plot in centimeters after shelling (i.e. with the kernels removed from the cob). This information for hybrids at the Scottsbluff, North Platte, Lincoln, and Missouri Valley locations was taken from the file ‘plotleveleardata_v2.csv’. Plot 426 in North Platte1 was dropped as all underlying observations were an order of magnitude larger than all other observations. Observations where shelledCobWidth was greater than earWidth were dropped. This information for the Ames and Crawfordsville locations was taken from the files in the folder ‘5 Cob Traits Station’ and converted from millimeters to centimeters.
kernelsPerRow
This is the mean number of kernels in each kernel row. This information for hybrids at the Scottsbluff, North Platte, Lincoln, and Missouri Valley locations was taken from the file ‘plotleveleardata_v2.csv’. This information was not collected for the Ames and Crawfordsville locations. Plot 4209 at Lincoln was calculated using 3 ears rather than 4 as the remaining observation was an order of magnitude larger than the others.
kernelRowNumber
This is the mean number of kernel rows, i.e. the number of kernels around the circumference of the ear at the middle of the ear. This information for hybrids at the Scottsbluff, North Platte, Lincoln, and Missouri Valley locations was taken from the file ‘plotleveleardata_v2.csv’. This information for the Ames and Crawfordsville locations was taken from the files in the folder ‘2 KRN And Ear Documentation’. Plots 367 and 866 at North Platte was calculated using 3 ears rather than 4 as the remaining observation was an order of magnitude larger than all others.
kernelsPerEar
This is the mean number of kernels per ear from the plot. It does not account for kernels that fell off the cob between harvest and phenotyping. This information for hybrids at the Scottsbluff, North Platte, Lincoln, and Missouri Valley locations was taken from the file ‘plotleveleardata_v2.csv’. Plot 1381 at North Platte was calculated using 3 ears rather than 4 as the remaining observation was an order of magnitude larger than the other observations. This information for the Ames and Crawfordsville locations was taken from the files in the folder ‘6 Seed Traits Station’.
hundredKernelMass
This is the mean weight of one hundred kernels from one ear from the plot in grams after to shelling (i.e. with the kernels detached from the cob). This information for hybrids at the Scottsbluff, North Platte, Lincoln, and Missouri Valley locations was taken from the file ‘plotleveleardata_v2.csv’. For the Ames and Crawfordsville locations, this was calculated as the mean kernel mass divided by the mean number of kernels per ear multiplied by one hundred. Plots 5122 and 5245 at Lincoln, and 835, 838, 1169, and 1211 at North Platte were calculated using 3 ears rather than 4, as the remaining observation was an order of magnitude larger than the others.
kernelMass
This is the mean mass of kernels in grams, per ear. For the North Platte, Scottsbluff, Lincoln, and Missouri Valley locations, this is calculated as the difference between the ear weight and shelled cob weight. This information for hybrids at the Scottsbluff, North Platte, Lincoln, and Missouri Valley locations was taken from the file ‘plotleveleardata_v2.csv’. Plot 256 at Missouri Valley and plot 664 at North Platte were calculated using 3 ears rather than 4 as the remaining observation was an order of magnitude larger than the other observations. This information for the Ames and Crawfordsville locations was taken from the files in the folder ‘6 Seed Traits Station’. In these two locations, the measured seed weight was used. In the cases that significant spillage was denoted, the difference between the ear weight and the shelled cob weight was used. Some ears’ kernels were re-weighed due to an off-balance scale. In this case, the re-weighing values replaced the original values.
shelledCobMass
This is the mean weight of the cob in grams of one ear from the plot after to shelling (i.e. with the kernels detached from the cob). Plot 1226 at North Platte was calculated using 3 rather than 4 ears as the remaining observation was an order of magnitude larger than all other observations. This information for hybrids at the Scottsbluff, North Platte, Lincoln, and Missouri Valley locations was taken from the file ‘plotleveleardata_v2.csv’. This information for the Ames and Crawfordsville locations was taken from the files in the folder ‘5 Cob Traits Station’.
percentMoisture
This is the percent moisture measured by NIR. For the Lincoln, Missouri Valley, North Platte, and Scottsbluff locations, this information was taken from the file ‘HybridHIPS_plotlevelNIR_v2.5.csv’. This information was not collected for the Ames and Crawfordsville locations. It is abbreviated as ‘pctMoistureNIR’.
percentStarch
This is the median proportion of the grain composed of starch as a percent of dry matter as measured by NIR spectrometry. In Missouri Valley, five replicates per plot were used, and three replicates per plot were used in all other locations. In the case any NIR measurement for a replicate was less than zero, this entire replicate was dropped prior to computing the median. This information for hybrids was taken from the file ‘HybridHIPS_plotlevelNIR_v2.xlsx’. This information was not collected for the Ames and Crawfordsville locations.
percentProtein
This is the median proportion of the grain composed of protein as a percent of dry matter as measured by NIR spectrometry. In Missouri Valley, five replicates per plot were used, and three replicates per plot were used in all other locations. In the case any NIR measurement for a replicate was less than zero, this entire replicate was dropped prior to computing the median. This information for hybrids was taken from the file ‘HybridHIPS_plotlevelNIR_v2.xlsx’. This information was not collected for the Ames and Crawfordsville locations.
percentOil
This is the median proportion of the grain composed of oil as a percent of dry matter as measured by NIR spectrometry. In Missouri Valley, five replicates per plot were used, and three replicates per plot were used in all other locations. In the case any NIR measurement for a replicate was less than zero, this entire replicate was dropped prior to computing the median. This information for hybrids was taken from the file ‘HybridHIPS_plotlevelNIR_v2.xlsx’. This information was not collected for the Ames and Crawfordsville locations.
percentFiber
This is the median proportion of the grain composed of fiber as a percent of dry matter as measured by NIR spectrometry. In Missouri Valley, five replicates per plot were used, and three replicates per plot were used in all other locations. In the case any NIR measurement for a replicate was less than zero, this entire replicate was dropped prior to computing the median. This information for hybrids was taken from the file ‘HybridHIPS_plotlevelNIR_v2.xlsx’. This information was not collected for the Ames and Crawfordsville locations.
percentAsh
This is the median proportion of the grain composed of ash as a percent of dry matter as measured by NIR spectrometry. In Missouri Valley, five replicates per plot were used, and three replicates per plot were used in all other locations. In the case any NIR measurement for a replicate was less than zero, this entire replicate was dropped prior to computing the median. This information for hybrids was taken from the file ‘HybridHIPS_plotlevelNIR_v2.xlsx’. This information was not collected for the Ames and Crawfordsville locations.
kernelColor
This is the color of the kernels from the plot. This information for hybrids was taken from the file ‘plotleveleardata_v2.csv’. This data was not collected for the Ames and Crawfordsville locations.
percentLodging
This is the percent of plants that lodged in the middle two rows of the plot for hybrids and in the whole plot for inbreds. This information for Missouri Valley, Crawfordsville, and Ames was taken from the sheets ‘RawData (4-Row)’ and ‘RawData (2-Row)’ for hybrids and inbreds, respectively, in the file ‘YTMC_Lisa_Plot_Coordinates_v4.xlsx’. This information for North Platte was taken from the sheets ‘No Irr Data’, ‘Reduced Irr Data’, and ‘Full Data’ in the file ‘2022_Schnable_HIPS_data_v4.xlsx’. This data was not collected at the Scottsbluff and Lincoln locations.
harvestDate
This is the date and time the plot was harvested by the combine. Inbred plots were not harvested by the combine. This information for the Lincoln location was taken from the sheet ‘Combined Dataset’ in the file ‘Summary of Lincoln Hybrid HIPS 2022 Data.xlsx’. For the Scottsbluff location, this information was taken from the file ‘Dipak Corn22_HM.xlsx’. For the Missouri Valley, Ames, and Crawfordsville locations, this data was taken from the file ‘YTMC_Lisa_Plot_Coordinates_v4.xlsx’. This information for North Platte was taken from the sheets ‘No Irr Data’, ‘Reduced Irr Data’, and ‘Full Data’ in the file ‘2022_Schnable_HIPS_data_v4.xlsx’.
notes
This contains any notes regarding the the plot. This information was aggregated across all notes columns for a plot in the original data files.
Location Notes
Lincoln
The alley length in both the Inbred HIPS and Hybrid HIPS fields was 2.5 feet, and the distance between seeds in a row was 6 inches. Nitrogen application was made on March 29, 2022 at the treatment-specified rates (Low: 75 lbs/acre, Medium: 150 lbs/acre, High: 225 lbs/acre) with urea ammonium nitrate (32-0-0) Conventional tillage was done prior to planting.
Inbred HIPS field
Plots in the Inbred HIPS field were 10 feet long center to center, including 7.5 feet of plants and 2.5 feet of alley. The planting date was May 5, 2022. Plots were hand-harvested (4 ears per plot) on October 8, 2022. The previous crop in the field was soybeans. The GPS coordinates for the field corners were:
NE corner: 40°51’32.96”N, 96°35’50.40”W
SW corner: 40°51’31.39”N, 96°35’54.10”W
NW Corner: 40°51’32.93”N, 96°35’54.10”W
SE Corner: 40°51’31.44”N, 96°35’50.36”W
Plots were two-row plots, and the field contained 16 plots (160 feet) north to south and 58 plots (290 feet) east to west.
Hybrid HIPS field
Plots in the Hybrid HIPS field were 20 feet long center to center, including 17.5 feet of plants and 2.5 feet of alley. The planting date was May 22, 2022. Plots were hand-harvested (4 ears per plot) on October 1, 2022 and combine harvested on October 10, 2022. The previous crop in the field was maize. The GPS coordinates for the field corners were:
NE corner: 40°51’8.59”N, 96°36’50.26”W
SW corner: 40°51’7.25”N, 96°37’0.54”W
NW Corner: 40°51’8.70”N, 96°37’0.52”W
SE Corner: 40°51’7.12”N, 96°36’50.29”W
The field was 150 feet north to south and 800 feet east to west. Differential weed pressure existed throughout the field according to James.
Missouri Valley
175 lbs of urea was applied on both the hybrid and inbred fields in this location. The nitrogen fertilizer was applied on June 6, 2022. The field latitude is 41.671747 N and the longitude is -95.943982 W. The fields were not irrigated. Planting was completed on April 29, 2022 and the harvest was completed on October 11, 2022. The previous crop for was corn.
Inbred HIPS field
There were 752 plots (376 plots per replication) in this field. The plots were two-row plots. The plot numbers shown in the image correspond to those used in the QR codes.
Hybrid HIPS field
There were 176 plots (88 plots per replication) in this field. The
plots were four-row plots. 
The plot numbers shown in the image correspond to those used in the QR codes. The QR codes mis-assigned the replicate numbers. These have been fixed in the dataset.
North Platte
Only the Hybrid HIPS population was grown at this location. Plot numbers are unique across the North Platte location, but range and row numbers were duplicated in each field. Each field is a different irrigation treatment. To account for this, the location was split in 3 by irrigation treatment in the data. North Platte1 is the full irrigation field; North Platte2 is the partial irrigation field, and North Platte3 is the dryland, i.e. rainfed, field. The plots were 4-row, 20 foot plots, with 17 feet of the plot planted and 3 feet of alley. Nitrogen treatments were blocked within each irrigation treatment. The full irrigation field was planted on May 17, 2022, and harvested on October 21, 2022 and November 1, 2022 with planted plot lengths of 17.5 feet. The partial irrigation field was planted on May 17, 2022 and harvested October 26 - 28, 2022 with planted plot lengths of 17.5 feet. The dryland field was planted on May 18, 2022 and harvested on October 19-21 and 24, 2022 with planted plot lengths of 17 feet. The previous crop was soybeans. Nitrogen was applied on June 16, 2022 as 32-0-0 with a 360 Y drop applicator.
In the image above, the blue rectangle is the approximate location of the full irrigation field, the yellow rectangle is the approximate location of the partial irrigation field, and the red rectangle is the approximate location of the dryland field.
The irrigation amounts and timing for the full and partial fields is as follows:
Scottsbluff
The field was irrigated for one hour from 4:00 p.m. to 5:00 p.m. every Friday evening, for a total of 16.86 inches of irrigation provided over the growing season.. The row spacing was 30”. In-field measurements (flowering time, height data, and combine yield measurements) use the range-row system defined in the sheet ‘Layout (Original)’ of the files ‘Scottsbluff Hybrid HIPS - Summary.xlsx’ and ‘Scottsbluff Inbred HIPS - Summary.xlsx’. In the data, these range-row assignments were dropped in favor of using the range-row assignments listed in the QR codes and used by the ear phenotype and NIR grain composition measurements, which better capture the spatial distance between plots where there are border plots. The geographic location within the field of a plot by its plot number is the same in both layouts, but the range-row numbering is different. The range-row system used in the QR codes and the data is depicted in the sheet ‘Layout (Modified)’ of the files ‘Scottsbluff Hybrid HIPS - Summary’ and ‘Scottsbluff Inbred HIPS - Summary.xlsx’, and shown in the image below. ‘Fill’ is equivalent to ‘Border’ at other locations. The field was planted north to south and together, the inbred and hybrid fields are 625 feet north to south. The fields were planted on May 19, 2022. A combination of 10-34-0 (NPK) liquid fertilizer and urea were applied to meet the nitrogen treatment level requirements, as shown below. Urea applications were made on July 8, 2022. Both field layouts denote that planting of the hybrid plots started in the southeast corner of the field; however, the correlations between two replicates of a genotype within a treatment indicate that planting started in the southwest corner of the field. The inbreds were still located directly to the west of the hybrids. In the corrected layout, plot 1001 is in the SW corner of the field, plot 1025 is in the NW corner of the field, the NE corner of the field is a fill plot, and plot 1491 is in the SE corner of the field. The previous crop was dry beans.
Inbred HIPS field
The plots were 10 foot (7.5 feet planted), 2-row plots. This field was very weedy according to Ramesh.
Hybrid HIPS field
Based on yield data and grain protein content, it was determined that the labels in the QR codes for the high and low nitrogen treatments were reversed. The QR codes in the data reflect the content of the original QR codes, and the nitrogen treatment variable reflects the actual level of nitrogen the plot received. The plots were 25 foot (22.5 feet planted), 4-row plots and the middle two rows were harvested.
Crawfordsville
These fields were planted on May 11, 2022 and harvested on October 7, 2022. Both the inbred and hybrid fields had 3 nitrogen treatments (High, Medium, and Low). The field coordinates were 41.199066, -91.486991. The nitrogen treatments were applied on June 2, 2022 using 32% UAN.
Field A - Low and High Nitrogen
Low nitrogen is to the west in these maps. The previous crop was soybeans.
Field B - Medium Nitrogen
The previous crop was soybeans.
Ames
These fields were planted on May 23, 2022 and harvested on October 16, 2022. Both the inbred and hybrid fields had 3 nitrogen treatments (High, Medium, and Low). The High and Medium nitrogen treatments for both hybrids and inbreds were located in the B1 field. The Low nitrogen treatments for both hybrids and inbreds were located in the E1 field.
B1
This field was planted on May 22, 2022. Nitrogen was applied using urea and 32% UAN on May 17, 2022, and June 1, 2022. The field coordinates were 42.015354, -93.732519. The previous crop was corn.
E1
This field was planted on May 23, 2022. Nitrogen was applied using urea on May 21, 2022. The field coordinates were 42.012376, -93.737301. The previous crop was soybeans.
Additional Data Available
Upon request, the following data is available:
Data Generation and Processing Notes
The following may be helpful in case of questions:
Jon Turkus generated the Excel file ‘Summary of Lincoln Hybrid HIPS 2022 Data.xlsx’ and collected the agronomic metadata for Lincoln.
Collection of NIR measurements were led by Chidanand Ullagaddi.
Collection of ear phenotypes post-harvest for the Scottsbluff, North Platte, Lincoln, and Missouri Valley locations was led by Lina López.
All data for the Ames and Crawfordsville were collected by the ISU Schnable Lab and/or the yield trial provider. Plant height data for Missouri Valley was collected by Huyu Liu and undergraduate students from the ISU Schnable Lab.
Ramesh Kanna provided in-field measurements and agronomic data for the Scottsbluff location.
NIR data was cleaned and processed by James Schnable using the script ‘clean_combineNIR.py’.
Ear data was cleaned and summarized to a plot level by James Schnable using the script ‘parseears.py’.
Subsequently, all data was combined and cleaned by Jensina using the script ‘CombineHIPS22Data.R’.
Appendix
Documentation for Additional Data Available
Leaf Length
This is the length in centimeters of the ear leaf from the stalk to leaf tip of one plant from the plot. It is abbreviated as ‘leaf_len1’. This information for the Lincoln location was taken from the sheet ‘Combined Dataset’ in the file ‘Summary of Lincoln Hybrid HIPS 2022 Data.xlsx’.
Leaf Width
This is the width in centimeters of the midpoint of the ear leaf of one plant from the plot. It is abbreviated as ‘leafWidth1’. This information for the Lincoln location was taken from the sheet ‘Combined Dataset’ in the file ‘Summary of Lincoln Hybrid HIPS 2022 Data.xlsx’.
Ear
This is the order the ears were phenotyped. It is abbreviated in the code as ‘earNum’, but does not appear in the final dataset as the ear data was transformed to have four columns each for ear width, kernel fill length, kernel row number, kernels per row, ear weight, seed color, total kernel count, cob length, cob width, cob weight, and 100 kernel weight. These variables with the suffix ‘1’ correspond to ears with an ear number of 1 in the dataset, and this convention is maintained for the variable suffixes 2-4. All ears with an ear number greater than 4 were dropped to create a balanced dataset.
Ear Weight
This is the weight of one ear from the plot in grams prior to shelling (i.e. with the kernels attached to the cob). This corresponds to the ear with an ear number of 1 from the original dataset. It is abbreviated as ‘earWt1’. This information for Lincoln hybrids, Missouri Valley hybrids and inbreds, and some of the North Platte location, was taken from the file ‘2022_Hybrid HIPS - Post Harvest Data - Prototype File.csv’. Information for the remaining ears from North Platte and the Scottsbluff hybrids were taken from the file ‘NP-SB_2022’.
Ear Drop Number
This is the number of ears that fell to the ground in the middle two rows of the plot for hybrids. It is abbreviated as ‘earDropNum’. This information for North Platte was taken from the sheets ‘No Irr Data’, ‘Reduced Irr Data’, and ‘Full Data’ in the file ‘2022_Schnable_HIPS_data_v4.xlsx’.
Stand Count 1
This is the number of standing plants in one row of the plot. It is abbreviated as ‘standCt1’. This information for Missouri Valley was taken from the sheets ‘RawData (4-Row)’ and ‘RawData (2-Row)’ for hybrids and inbreds, respectively, in the file ‘YTMC_Lisa_Plot_Coordinates_v4.xlsx’. This information for North Platte was taken from the sheets ‘No Irr Data’, ‘Reduced Irr Data’, and ‘Full Data’ in the file ‘2022_Schnable_HIPS_data_v4.xlsx’.
Stand Count 2
This is the number of standing plants in a second row of the plot. It is abbreviated as ‘standCt2’. This information for Missouri Valley was taken from the sheets ‘RawData (4-Row)’ and ‘RawData (2-Row)’ for hybrids and inbreds, respectively, in the file ‘YTMC_Lisa_Plot_Coordinates_v4.xlsx’. This information for North Platte was taken from the sheets ‘No Irr Data’, ‘Reduced Irr Data’, and ‘Full Data’ in the file ‘2022_Schnable_HIPS_data_v4.xlsx’.
Historical Flowering Time
This is the historical flowering time, in days, of the inbred and was used to for blocking the inbreds. It is abbreviated as ‘histFT’. This information was taken from the sheet ‘RawData (2-Row)’ in the file ‘YTMC_Lisa_Plot_Coordinates_v4.xlsx’.
Historical Plant Height
This is the historical plant height, in centimeters, of the inbred, and was used for blocking the inbreds. It is abbreviated as ‘histPlantHt’. This information was taken from the sheet ‘RawData (2-Row)’ in the file ‘YTMC_Lisa_Plot_Coordinates_v4.xlsx’.
Inbred Block
This is the block the inbred was placed in based on historical plant height and days to flowering. It is abbreviated as ‘block’. This information was taken from the sheet ‘RawData (2-Row)’ in the file ‘YTMC_Lisa_Plot_Coordinates_v4.xlsx’.
Population
This is the genotypic population the plants grown in the plot are from, either the Hybrid HIPS population, abbreviated as ‘Hybrid’, or the Inbred HIPS population, also known as the SAM population, abbreviated as ‘Inbred’. It is abbreviated as ‘population’.
Ear Length - Pre-Shelling
This is the mean length of the ear prior to shelling (i.e. with the kernels on the ear) of one ear from the plot. It is abbreviated as ‘earLen’. This information for the Ames and Crawfordsville locations was taken from the files in the folder ‘3 Ear Traits Station’ and converted from millimeters to centimeters. For these two locations, when the ear had severe bending, a string was used to measure the length and this is denoted in the notes field. This data was not collected at the North Platte, Scottsbluff, Lincoln, and Missouri Valley locations.
Tassel Tip Height
This is the height in centimeters of the plant, including the tassel, of one plant from the plot (in the case of Scottsbluff) or the average of this measurement for two plants from the plot in Lincoln. All measurements from plants noted as stunted or without a silk were marked as missing data prior to calculation. It is abbreviated as ‘tasselTipHt’. This information for the Lincoln location hybrids was taken from the sheet ‘Combined Dataset’ in the file ‘Summary of Lincoln Hybrid HIPS 2022 Data.xlsx’. For Scottsbluff hybrids, this data was taken from the sheet ‘Hybrid_height data’ from the file ‘Corn_data_Scottsbluff-2022_rk_11.11.2022’ and converted from inches. Plot 1322 at the Scottsbluff location was dropped due to having a value more than 114 centimeters (roughly 3.7 feet) greater than all other observations.
KernelStriping
This is whether or not the kernels from the plot exhibited striping. It is abbreviated as ‘kernelStriping’. This information for hybrids and Missouri Valley inbreds was taken from the file ‘plotleveleardata_v2.csv’. This information was not collected for the Ames and Crawfordsville locations.
Percent Shoot Lodge
This is the percent of plants that lodged due to stalk breakage in the middle two rows of the plot for hybrids and in the whole plot for inbreds. It is abbreviated as ‘pctStalkLodge’. This information for Missouri Valley, Crawfordsville, and Ames was taken from the sheets ‘RawData (4-Row)’ and ‘RawData (2-Row)’ for hybrids and inbreds, respectively, in the file ‘YTMC_Lisa_Plot_Coordinates_v4.xlsx’. This information for North Platte was taken from the sheets ‘No Irr Data’, ‘Reduced Irr Data’, and ‘Full Data’ in the file ‘2022_Schnable_HIPS_data_v4.xlsx’.
Percent Root Lodge
This is the percent of plants that lodged due to insufficient roots in the middle two rows of the plot for hybrids and in the whole plot for inbreds. It is abbreviated as ‘pctStalkLodge’. This information for Missouri Valley, Crawfordsville, and Ames was taken from the sheets ‘RawData (4-Row)’ and ‘RawData (2-Row)’ for hybrids and inbreds, respectively, in the file ‘YTMC_Lisa_Plot_Coordinates_v4.xlsx’. This information for North Platte was taken from the sheets ‘No Irr Data’, ‘Reduced Irr Data’, and ‘Full Data’ in the file ‘2022_Schnable_HIPS_data_v4.xlsx’.